X-ray Crystallographic Data ............................................................................................. 27
Aranda IV, Roman,
Levin, Elena J.
2. Using Low
Complexity Regions for Target Selection in Structural Genomics................... 28
3. Simulating
Nucleic Acids: Comparison Between Explicit, Implicit
and Hybrid Solvation
Models............................................................................................ 29
4. Folding Proteins by Constrained
Minimization of a Statistical
Potential
of Mean Force.................................................................................................................... 30
5. Effect of Sequence Length and Number of Taxa
on Phylogeny
SimDB:
The Simulation Database..................................................................................... 31
6. A Model for Binding of Capping Protein to Barbed End of Actin...................................... 32
7. Rapid Computational Prediction of the Substrates of cAMP-dependent
Protein
Kinase.................................................................................................................... 33
8. Molecular Dynamics Simulations of Phospholamban: Effects of Membrane,
Phosphorylation
and Aggregation....................................................................................... 34
9. Predisposition
of the Three-Dimensional Dark State Structure of Rhodopsin for
Functional Conformational
Changes................................................................................... 35
10. The “other half” of the Folded
State of Proteins................................................................. 36
11.
Identifying
Favourable Candidate Molecules Using Statistical Physics.............................. 37
12. Finding Alternate Binding Conformations in Proteins: A Molecular
Dynamics and
Docking
Study of p38 MAP Kinase.................................................................................... 38
13. Protein Structure-Sequence Alignment with a Reliability
Measure.................................... 39
14. Mechanism of Control of Small Ligand Release in
Nitrophorin and
Myoglobin.......................................................................................................................... 40
X-ray Crystallographic Data.............................................................................................. 41
Levin, Elena and Aranda IV, Roman
16. A Molecular Dynamics Free Energy Study of the
Large-scale Motion of Adenylate Kinase 42
17. Application of Rough Set Theory to the Analysis of
Chemically-Induced Gene
Expression Patterns............................................................................................................ 43
18. Atomically Detailed Simulations
of Concentrated Protein Solutions:
Capturing the Effects of
pH, Ionic Strength and Point Mutations........................................ 44
19. Binding
of Dinitroanilines to a-Tubulin of Protozoan Parasites via Computational
Modeling............................................................................................................................ 45
20. Characterization of Internal and Global Dynamics of
HIV-1 TAR RNA by
Molecular Dynamics and NMR.......................................................................................... 46
21. An
Efficient Iterative Cost-Bounded Branch-and-Bound Search Algorithm for
Solving
Discrete Optimization Problems in Computational Biology
Namilikonda,
Sandeep K............................................................................................... 47
22. Effect of Domain-domain
Interactions on Src Family Tyrosine Kinase
Activation........................................................................................................................... 48
23. Structural
Insights into Mechanism of Actin based Cell Motility Via Computational
24. Rapid Computational Identification of the
Targets of Protein Kinase Inhibit...................... 50
25. Human Topoisomerase I Relaxes
Positive and Negative DNA Supercoils Differently....... 51
26.
Molecular Dynamic Simulations of the Wild
Type and Mutant (D25N) HIV Protease:
27. A
Multiscale Model for Actin Filaments............................................................................. 53
28. Structural
Determinants of Brugia malayi
Asparaginyl tRNA Synthetase Affinity and
29. Free
Energy of G76 and the Mutants Rotation in Hepatitis Delta Virus
Ribozyme............................................................................................................................ 55
30.
Replica Exchange Molecular Dynamics
Simulations Coupled with the Heterogeneous
31. Molecular
Dynamics Simulations of Salt on Small Molecule Associations:
Implicit Models................................................................................................................... 57
32.
Repetitive Pulling Catalyzes
Co-Translocational Unfolding of Barnase During Import
33. New Developments in Empirical Scoring Function:
X-Score Version 2005...................... 59
34. The PDBbind Database: A PDB-Wide Collection of Protein-Ligand Binding Affinities... 60
35. Functional
Importance of Protein Dynamics in Enthalpy-Entropy
Compensation................................................................................................................ 61
36.
SoftScore: A New Knowledge-Based Potential Scoring
Function by Inclusion of the
37. A Molecular Dynamics Exploration of Dihydroneopterin
Aldolase and the Exit Path